Purpose: This study aims to address the limitations of conventional malaria diagnosis—namely, its reliance on manual microscopy, which is time-consuming, labor-intensive, and prone to human error—by developing an automated diagnostic system using the Inception V3 convolutional neural network. The focus is on accurately identifying the four main Plasmodium species responsible for malaria (P. falciparum, P. malariae, P. ovale, and P. vivax) through image-based analysis of red blood cells. The study’s significance lies in its contribution to scalable, AI-assisted diagnostic solutions that support national and global malaria elimination goals, particularly in high-burden countries such as Indonesia. Methods: This study utilized an experimental approach based on a dataset of 194 microscopic images of red blood cells, each labeled according to one of four Plasmodium species. The process involved image enhancement through pre-processing techniques—illumination correction, contrast adjustment, and noise filtering—followed by segmentation using the Otsu thresholding method to isolate parasite-infected cells. Two classification models were applied: Inception V3, a deep learning convolutional neural network, and a traditional Support Vector Machine (SVM), with both evaluated for their accuracy in species identification. Result: The findings revealed that the Inception V3 model significantly outperformed the Support Vector Machine (SVM), achieving highest accuracy of 100%, at select epochs and an average accuracy of 97.93%, with 98.32% validation accuracy compared to 82% for SVM. The high performance of Inception V3 is attributed to its deep architecture, consisting of over 23 million parameters, which enables superior feature extraction and classification of Plasmodium species. These results confirm that CNN-based models, particularly Inception V3, are more effective than traditional machine learning approaches for automated malaria diagnosis. Novelty: In identifying four species of Plasmodium, this study presents a very simple yet highly accurate technique using an Inception V3 model. The method represents 100% accuracy in its multi-class detection as opposed to earlier works concentrating on binary classifications. It therefore adds real usefulness in high-burden, low-resource settings such as Indonesia through working on the improvement of diagnosis and on speedier detection of malaria.